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M.C.J. Ma et al.
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Figure 3. Functional enrichment of tar- gets of somatic mutations and DNA copy number alterations. Genes target- ed by somatic mutation and/or DNA copy number alteration were evaluated for enrichment in curated gene sets, and significant gene sets subsequently grouped according to overlapping gene set membership and functional similari- ty. In addition to genes assigned by DAVID (purple), some genes were man- ually curated into hallmark processes by literature review of their function (pink). Enriched gene sets could be summarized into four major hallmark processes, including (A) epigenetic and transcriptional control of gene expres- sion, (B) regulation of apoptosis and proliferation, (C) regulation of signaling pathway activity, and (D) regulation of protein ubiquitination. The frequency of each genetic alteration is shown for each of the four major histologies included in this study, and the fraction of tumors in each histology bearing genetic alterations of one or more of the genes is summarized by a pie graph at the bottom for each hallmark. BL: Burkitt lymphoma; DLBCL: diffuse large B-cell lymphoma; FL: follicular lym- phoma; MCL: mantle cell lymphoma; HMT, histone methyltransferase. HAT, histone acetyltransferase. DDR, DNA damage response. BCR, B-cell receptor.
Furthermore, Cluster 2 and Cluster 4 alterations were cumulatively acquired in 58% of ABC-like DLBCL and 60% of GCB-like DLBCL, respectively, further supporting their respective overlap with the C5/MCD/MYD88 and C4/ST2 subtypes of DLBCL. CNA within Cluster 5 were cumulatively acquired at high but variable frequencies in all of the subtypes, but showed subtype-specific patterns within this cluster such as higher frequencies of 18q21 and 18q23 gains in ABC-like DLBCL, and higher frequencies of chromosome 7 gains in GCB-like DLBCL and FL. B-NHL tumors therefore cumulatively acquire co-associated sets of genetic alterations in a manner that is characteristically associated with histologically- and molecularly-defined subsets of disease.
Discussion
By performing cross-sectional genomic profiling of a large cohort of tumors, we have developed a resource of genes and functional hallmarks that are recurrently targeted by genetic alterations in B-NHL, and have shown that the cumulative acquisition of combinations of genetic alter- ations are characteristic of histological and molecular sub- types of disease. Some of the functional hallmarks that we identified have been previously appreciated, with a few exceptions. For example, the mutation of genes with roles
Combinations of genetic alterations define molecular subtypes of B-cell non-Hodgkin lymphoma
Our data have revealed statistical enrichment of individ- ual genetic alterations in subtypes of B-NHL, and pairwise relationships between different genetic alterations that define clusters of subtype-specific events. To validate and expand upon these observations we leveraged gene expres- sion microarray data from 284 tumors that underwent pathology review and were profiled as part of prior stud- ies.10-12 We utilized BL, DHL, HGBL-NOS and DLBCL tumors to perform classification into molecularly-defined BL (mBL) and non-mBL using a Bayesian classifier with pre- viously described marker genes,51 and subclassified non- mBL into activated B-cell (ABC)-like and GCB-like subtypes as we have described previously26 (Online Supplementary Figure S7). We evaluated the frequency of cumulative (≥2) genetic alterations within each cluster among mBL, ABC- like DLBCL, GCB-like DLBCL, FL and MCL (Figure 6). This showed that Cluster 1 genetic alterations that were individ- ually enriched in BL are cumulatively acquired in mBL, with 87% of tumors having ≥2 of these alterations compared to only 22% of GCB-like DLBCL. Similarly, Cluster 4 and Cluster 7 alterations were cumulatively acquired in 77% and 72% of molecularly-annotated FL and MCL, respec- tively. Cluster 4 mutations were also cumulatively acquired in 51% of GCB-like DLBCL, likely capturing the C3/EZB/BCL2 subtype that has genetic similarities to FL.3,4,50
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haematologica | 2022; 107(3)